A rapid and simple in situ test for RNA integrity in Formalin-Fixed Paraffin Embedded (FFPE) will be developed in order to facilitate the selection of well-annotated, archival FFPE clinical samples with high quality RNA for gene expression analysis. The ratio of fluorescence signal from Quenched Auto Ligation (QUAL) probes of different lengths will be used to assess the degree of RNA fragmentation in FFPE samples in situ, prior to cumbersome and time- consuming RNA extraction. The Quality Control (QC) metric from the QUAL probes will be correlated to the quality of downstream gene expression analysis by RT-PCR and microarray on RNA extracted from the FFPE samples assayed for RNA integrity. The eventual goal is to develop and commercialize a QC kit for FFPE sample RNA quality. This research will aid and accelerate the discovery of more accurate molecular biomarkers for detection, prognosis and treatment of cancer. PUBLIC HEALTH RELEVANCE: "One Step In Situ RNA Integrity Analysis for FFPE Tissue". There are millions of potentially valuable, well-annotated clinical pathology samples around the world many of which cannot be used for clinical studies because of poor sample quality. The proposed research will enable more accurate detection, prognosis and treatment of cancer by improving the accuracy of selecting only high quality archival pathology samples for molecular analysis. The development of a simple and rapid, commercially available test to assess the quality of a pathology sample will also accelerate the pace of molecular studies needed for the discovery of drugs for cancer patients, and the detection of cancer in the general population in order to improve public health.